Cluster Identification

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Last updated: 2024-09-28

Checks: 7 0

Knit directory: files/

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Repository version: d26f449

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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/02_01_Clustering_scRNA.Rmd) and HTML (docs/02_01_Clustering_scRNA.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	8963c8b	Andreas Chiocchetti	2024-02-12	Build site.
Rmd	d6ec671	Andreas Chiocchetti	2024-02-12	wflow_publish(c("./analysis/.Rmd", "./code/", "./docs/", "output/"))
html	d6ec671	Andreas Chiocchetti	2024-02-12	wflow_publish(c("./analysis/.Rmd", "./code/", "./docs/", "output/"))
html	b307d09	Andreas Chiocchetti	2024-01-17	Build site.
Rmd	09c0f4c	Andreas Chiocchetti	2024-01-17	wflow_publish("./analysis/02_01_Clustering_scRNA.Rmd")
html	59bee55	Andreas Chiocchetti	2024-01-14	Build site.
html	472919f	Andreas Chiocchetti	2024-01-12	Build site.
html	9044a86	Andreas Chiocchetti	2024-01-11	Build site.
html	f206c28	Andreas Chiocchetti	2024-01-11	wflow_publish(c("./analysis/.Rmd", "./code/", "./docs/*"))
Rmd	bca1a73	Andreas Chiocchetti	2024-01-09	intermediate stage bulk seq

---

Clustering Analysis

Clustering after batch correction

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9383
Number of communities: 7
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9007
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8746
Number of communities: 14
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8516
Number of communities: 14
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8312
Number of communities: 16
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8164
Number of communities: 19
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8028
Number of communities: 20
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7900
Number of communities: 21
Elapsed time: 0 seconds

UMAP Clustering after batch correction at different resolutions

Past versions of unnamed-chunk-1-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Check stability of clusters

Past versions of unnamed-chunk-2-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 9107
Number of edges: 410519

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8746
Number of communities: 14
Elapsed time: 0 seconds

optimize UMAP

<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>
<simpleWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session>

Past versions of unnamed-chunk-4-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

final UMAP clustering

Past versions of unnamed-chunk-5-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Past versions of unnamed-chunk-6-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Calculate cell cycle scoring

Past versions of "Cell cycle scoring-1.png"

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Identification of clusters

Past versions of unnamed-chunk-8-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

          0mM       5mM
0mM 1.0000000 0.6908695
5mM 0.6908695 1.0000000

Past versions of unnamed-chunk-9-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Feature plots UMAP

Past versions of unnamed-chunk-10-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Feature plots PCA

Past versions of unnamed-chunk-11-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Markers identification and visualization

Past versions of "Identifying markers-1.png"

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

Visualizing the expression of marker genes with respect to different cell types

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

Past versions of unnamed-chunk-13-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
59bee55	Andreas Chiocchetti	2024-01-14
65a97d3	Andreas Chiocchetti	2024-01-13
f206c28	Andreas Chiocchetti	2024-01-11

chr 16p11 genes expression by cluster

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

Past versions of unnamed-chunk-14-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
b307d09	Andreas Chiocchetti	2024-01-17

16p11 genes PA condition

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

Past versions of unnamed-chunk-15-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
b307d09	Andreas Chiocchetti	2024-01-17

chr16p11 violin plots

Past versions of unnamed-chunk-16-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
b307d09	Andreas Chiocchetti	2024-01-17

Kynurenine genes expression by cluster

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

Past versions of unnamed-chunk-17-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
b307d09	Andreas Chiocchetti	2024-01-17

Kynurenine genes PA condition

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

Past versions of unnamed-chunk-18-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
b307d09	Andreas Chiocchetti	2024-01-17

Kynurenine violin plots

Past versions of unnamed-chunk-19-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
b307d09	Andreas Chiocchetti	2024-01-17

GO terms of clusters

[1] "result" "meta"  

Past versions of unnamed-chunk-20-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
b307d09	Andreas Chiocchetti	2024-01-17

Past versions of unnamed-chunk-21-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
b307d09	Andreas Chiocchetti	2024-01-17

Past versions of unnamed-chunk-22-1.png

Version	Author	Date
a41b1a6	Andreas Chiocchetti	2024-04-12
8963c8b	Andreas Chiocchetti	2024-02-12
d6ec671	Andreas Chiocchetti	2024-02-12
b307d09	Andreas Chiocchetti	2024-01-17

Session information

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] openxlsx_4.2.5.2            DESeq2_1.40.2              
 [3] pheatmap_1.0.12             compareGroups_4.8.0        
 [5] kableExtra_1.4.0            clustree_0.5.1             
 [7] ggraph_2.2.1                CATALYST_1.24.0            
 [9] reshape2_1.4.4              pals_1.8                   
[11] gprofiler2_0.2.3            viridis_0.6.5              
[13] viridisLite_0.4.2           cowplot_1.1.3              
[15] randomcoloR_1.1.0.1         RCurl_1.98-1.14            
[17] RColorBrewer_1.1-3          data.table_1.15.4          
[19] lubridate_1.9.3             forcats_1.0.0              
[21] stringr_1.5.1               dplyr_1.1.4                
[23] purrr_1.0.2                 readr_2.1.5                
[25] tidyr_1.3.1                 tibble_3.2.1               
[27] tidyverse_2.0.0             scater_1.28.0              
[29] scuttle_1.10.3              Seurat_5.0.3               
[31] SeuratObject_5.0.1          sp_2.1-3                   
[33] SingleCellExperiment_1.24.0 ggpubr_0.6.0               
[35] ggplot2_3.5.0               SingleR_2.2.0              
[37] SummarizedExperiment_1.32.0 Biobase_2.62.0             
[39] GenomicRanges_1.54.1        GenomeInfoDb_1.38.1        
[41] IRanges_2.36.0              S4Vectors_0.40.2           
[43] BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
[45] matrixStats_1.3.0           workflowr_1.7.1            

loaded via a namespace (and not attached):
  [1] dichromat_2.0-0.1           nnet_7.3-19                
  [3] goftest_1.2-3               DT_0.33                    
  [5] TH.data_1.1-2               vctrs_0.6.5                
  [7] spatstat.random_3.2-3       digest_0.6.35              
  [9] png_0.1-8                   shape_1.4.6.1              
 [11] git2r_0.33.0                ggrepel_0.9.5              
 [13] httpcode_0.3.0              deldir_2.0-4               
 [15] parallelly_1.37.1           fontLiberation_0.1.0       
 [17] MASS_7.3-60.0.1             httpuv_1.6.15              
 [19] foreach_1.5.2               withr_3.0.0                
 [21] ggrastr_1.0.2               xfun_0.43                  
 [23] survival_3.5-8              crul_1.4.2                 
 [25] memoise_2.0.1               ggbeeswarm_0.7.2           
 [27] RProtoBufLib_2.12.1         drc_3.0-1                  
 [29] systemfonts_1.0.6           ragg_1.3.0                 
 [31] zoo_1.8-12                  GlobalOptions_0.1.2        
 [33] gtools_3.9.5                V8_4.4.2                   
 [35] pbapply_1.7-2               promises_1.3.0             
 [37] httr_1.4.7                  rstatix_0.7.2              
 [39] globals_0.16.3              fitdistrplus_1.1-11        
 [41] ps_1.7.6                    rstudioapi_0.16.0          
 [43] pan_1.9                     miniUI_0.1.1.1             
 [45] generics_0.1.3              processx_3.8.4             
 [47] curl_5.2.1                  zlibbioc_1.48.0            
 [49] ScaledMatrix_1.8.1          polyclip_1.10-6            
 [51] GenomeInfoDbData_1.2.11     SparseArray_1.2.2          
 [53] xtable_1.8-4                doParallel_1.0.17          
 [55] evaluate_0.23               S4Arrays_1.2.0             
 [57] glmnet_4.1-8                hms_1.1.3                  
 [59] irlba_2.3.5.1               colorspace_2.1-0           
 [61] ROCR_1.0-11                 reticulate_1.36.0          
 [63] spatstat.data_3.0-4         magrittr_2.0.3             
 [65] lmtest_0.9-40               later_1.3.2                
 [67] lattice_0.22-6              mapproj_1.2.11             
 [69] spatstat.geom_3.2-9         future.apply_1.11.2        
 [71] getPass_0.2-4               scattermore_1.2            
 [73] XML_3.99-0.16.1             RcppAnnoy_0.0.22           
 [75] pillar_1.9.0                nlme_3.1-164               
 [77] iterators_1.0.14            compiler_4.3.1             
 [79] beachmat_2.16.0             RSpectra_0.16-1            
 [81] stringi_1.8.3               jomo_2.7-6                 
 [83] minqa_1.2.6                 tensor_1.5                 
 [85] plyr_1.8.9                  crayon_1.5.2               
 [87] abind_1.4-5                 truncnorm_1.0-9            
 [89] chron_2.3-61                locfit_1.5-9.9             
 [91] graphlayouts_1.1.1          sandwich_3.1-0             
 [93] whisker_0.4.1               codetools_0.2-20           
 [95] multcomp_1.4-25             textshaping_0.3.7          
 [97] BiocSingular_1.16.0         openssl_2.1.1              
 [99] flextable_0.9.5             crosstalk_1.2.1            
[101] bslib_0.7.0                 GetoptLong_1.0.5           
[103] plotly_4.10.4               mime_0.12                  
[105] splines_4.3.1               circlize_0.4.16            
[107] Rcpp_1.0.12                 fastDummies_1.7.3          
[109] sparseMatrixStats_1.12.2    knitr_1.46                 
[111] utf8_1.2.4                  clue_0.3-65                
[113] lme4_1.1-35.2               fs_1.6.3                   
[115] listenv_0.9.1               checkmate_2.3.1            
[117] nnls_1.5                    DelayedMatrixStats_1.22.6  
[119] ggsignif_0.6.4              Matrix_1.6-5               
[121] callr_3.7.6                 tzdb_0.4.0                 
[123] svglite_2.1.3               tweenr_2.0.3               
[125] pkgconfig_2.0.3             tools_4.3.1                
[127] cachem_1.0.8                fastmap_1.1.1              
[129] rmarkdown_2.26              scales_1.3.0               
[131] grid_4.3.1                  ica_1.0-3                  
[133] officer_0.6.5               broom_1.0.5                
[135] sass_0.4.9                  patchwork_1.2.0            
[137] dotCall64_1.1-1             carData_3.0-5              
[139] rpart_4.1.23                RANN_2.6.1                 
[141] farver_2.1.1                tidygraph_1.3.1            
[143] yaml_2.3.8                  cli_3.6.2                  
[145] writexl_1.5.0               leiden_0.4.3.1             
[147] lifecycle_1.0.4             askpass_1.2.0              
[149] uwot_0.2.1                  mvtnorm_1.2-4              
[151] backports_1.4.1             BiocParallel_1.34.2        
[153] cytolib_2.12.1              timechange_0.3.0           
[155] gtable_0.3.4                rjson_0.2.21               
[157] ggridges_0.5.6              progressr_0.14.0           
[159] parallel_4.3.1              limma_3.56.2               
[161] jsonlite_1.8.8              mitml_0.4-5                
[163] RcppHNSW_0.6.0              bitops_1.0-7               
[165] openxlsx2_1.5               Rtsne_0.17                 
[167] FlowSOM_2.8.0               spatstat.utils_3.0-4       
[169] BiocNeighbors_1.18.0        zip_2.3.1                  
[171] flowCore_2.12.2             mice_3.16.0                
[173] jquerylib_0.1.4             highr_0.10                 
[175] lazyeval_0.2.2              shiny_1.8.1.1              
[177] ConsensusClusterPlus_1.64.0 htmltools_0.5.8.1          
[179] sctransform_0.4.1           gfonts_0.2.0               
[181] glue_1.7.0                  spam_2.10-0                
[183] XVector_0.42.0              gdtools_0.3.7              
[185] rprojroot_2.0.4             Rsolnp_1.16                
[187] gridExtra_2.3               boot_1.3-30                
[189] igraph_2.0.3                R6_2.5.1                   
[191] labeling_0.4.3              cluster_2.1.6              
[193] nloptr_2.0.3                DelayedArray_0.28.0        
[195] tidyselect_1.2.1            vipor_0.4.7                
[197] plotrix_3.8-4               maps_3.4.2                 
[199] xml2_1.3.6                  ggforce_0.4.2              
[201] fontBitstreamVera_0.1.1     car_3.1-2                  
[203] future_1.33.2               rsvd_1.0.5                 
[205] munsell_0.5.1               KernSmooth_2.23-22         
[207] fontquiver_0.2.1            htmlwidgets_1.6.4          
[209] ComplexHeatmap_2.16.0       rlang_1.1.3                
[211] spatstat.sparse_3.0-3       spatstat.explore_3.2-7     
[213] uuid_1.2-0                  colorRamps_2.3.4           
[215] HardyWeinberg_1.7.8         ggnewscale_0.4.10          
[217] fansi_1.0.6                 beeswarm_0.4.0